jamesaoverton
commented
1 year ago @cmungall and I talked about this a bit on Slack last week. @bpeters42 do you want to raise this issue on Monday's call, when you're chairing?
Open cmungall opened 1 year ago
jamesaoverton
commented
1 year ago @cmungall and I talked about this a bit on Slack last week. @bpeters42 do you want to raise this issue on Monday's call, when you're chairing?
bpeters42
commented
1 year ago That is a good idea.
On Wed, Mar 8, 2023 at 8:22 AM James A. Overton @.***> wrote:
@cmungall https://github.com/cmungall and I talked about this a bit on Slack last week. @bpeters42 https://github.com/bpeters42 do you want to raise this issue on Monday's call, when you're chairing?
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cmungall
commented
1 year ago One idea is to bring certain parts of obi (processes, material entities , data objects) to the foreground more. Perhaps a release subset with some bfo branches removed. I would go further but I understand there are users of the other branches
On Wed, Mar 8, 2023 at 12:13 PM bpeters42 @.***> wrote:
That is a good idea.
On Wed, Mar 8, 2023 at 8:22 AM James A. Overton @.***> wrote:
@cmungall https://github.com/cmungall and I talked about this a bit on Slack last week. @bpeters42 https://github.com/bpeters42 do you want to raise this issue on Monday's call, when you're chairing?
— Reply to this email directly, view it on GitHub <https://github.com/obi-ontology/obi/issues/1662#issuecomment-1460449805 , or unsubscribe < https://github.com/notifications/unsubscribe-auth/ADJX2ISC4BYX4KTSENWUFIDW3CW3NANCNFSM6AAAAAAVKJFN5I
. You are receiving this because you were mentioned.Message ID: @.***>
-- Bjoern Peters Professor La Jolla Institute for Immunology 9420 Athena Circle https://www.google.com/maps/search/9420+Athena+Circle+%0D%0ALa+Jolla,+CA+92037,+USA?entry=gmail&source=g La Jolla, CA 92037, USA https://www.google.com/maps/search/9420+Athena+Circle+%0D%0ALa+Jolla,+CA+92037,+USA?entry=gmail&source=g Tel: 858/752-6914 Fax: 858/752-6987 http://www.liai.org/pages/faculty-peters
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bpeters42
commented
1 year ago Thanks Chris, for the awesome writeup and the follow up. We have been attempting to do what you proposed a bit by favoring the 'planned process' branch over others. So for example we (should be) favoring the 'injection process' over the 'injection function'. And use a shortcut relation between the devices that have a function and the process that realizes it. As with everything OBI, implementing this requires someone driving it, and the current focus of our efforts has been on assays and specimens. Devices has been on our 'next to do list' for a while, but we are slow. At a minimum though, we should have the design pattern (and shortcut relation) apparent and documented in COB. We will discuss as a group Monday and get back to you.
On Thu, Mar 9, 2023 at 8:00 AM Chris Mungall @.***> wrote:
One idea is to bring certain parts of obi (processes, material entities , data objects) to the foreground more. Perhaps a release subset with some bfo branches removed. I would go further but I understand there are users of the other branches
On Wed, Mar 8, 2023 at 12:13 PM bpeters42 @.***> wrote:
That is a good idea.
On Wed, Mar 8, 2023 at 8:22 AM James A. Overton @.***> wrote:
@cmungall https://github.com/cmungall and I talked about this a bit on Slack last week. @bpeters42 https://github.com/bpeters42 do you want to raise this issue on Monday's call, when you're chairing?
— Reply to this email directly, view it on GitHub < https://github.com/obi-ontology/obi/issues/1662#issuecomment-1460449805 , or unsubscribe <
https://github.com/notifications/unsubscribe-auth/ADJX2ISC4BYX4KTSENWUFIDW3CW3NANCNFSM6AAAAAAVKJFN5I
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-- Bjoern Peters Professor La Jolla Institute for Immunology 9420 Athena Circle < https://www.google.com/maps/search/9420+Athena+Circle+%0D%0ALa+Jolla,+CA+92037,+USA?entry=gmail&source=g
La Jolla, CA 92037, USA < https://www.google.com/maps/search/9420+Athena+Circle+%0D%0ALa+Jolla,+CA+92037,+USA?entry=gmail&source=g
Tel: 858/752-6914 Fax: 858/752-6987 http://www.liai.org/pages/faculty-peters
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bpeters42
commented
1 year ago Discussed on call 3/13. The decision was made to follow Chris recommendations and document the use of our design patterns and clean up OBI in the process. The decision was made to do this as part of the OBI to COB migration, which should be used to document the high level classes of OBI in COB for the broader OBO community. 'Planned process' and 'device' would be the favored classes to create named subclasses for in OBI.
turbomam
commented
4 weeks ago reflection from today's call: if we started using a device template, we could impose consistent modeling
OBI frequently has the same concept or closely related concepts distributed across different BFO branches. Sometimes the different aspects are coordinated, and sometimes not:
The function branch doesn't appear to have any connection with the process or material branch, I can't find axioms connecting them. The ascribed function of a syringe doesn't seem to connect to the injection function, only to "transfer" (of course syringes can inject or withdraw, but it would seem to have both functions):
over on the process side, there is a connection to an objective branch, which is a 4th BFO branch under information/GDC, this branch seems to have a distinctly function-like aspect. However, while the "objective" of injection is to transform, in contrast to the "injection function", which is to transfer:
Is this distinction intentional or does it reflect the fact that the branches are old developed by different people at different times, etc? What is the use case for breaking things down into elemental concepts like transference, transformation?
the material and process branches appear to be a bit more synchronized; there is a complex axiom connecting syringe and injection:
injection EquivalentTo:
I think the intent here overall is to model the two things a syringe does - inject and withdraw. But it seems to require a lot of different branches with lots of abstract concepts (I have read the definition of material to be added role a few times and I am not sure I get it). And there are inconsistencies between the branches, it's not clear if this is intentional reflecting different nuances or just the fact it is hard to coordinate multiple branches.
For example:
injectionsays introducing a compound or a mixture into a material entity (either biological entity or instrument), but the owl says injection must be realized by a syringe which has more restrictive criteria (fluids)injectionsays it must be injected into a vascular system (which strangely includes machines) or tissues, but syringe is more lenient (any material entity)injectionsays by means of devices such as syringe or injector connection, but according to the OWL this is restricted to syringes (and what is an injector connection?)Here is a more zoomed out view:
I'm also confused about the duplication between objective and process hierarchies:
These seem to partially mirror one another, but with differences. There also don't seem to be linkages between shadow concepts, e.g. material combination and material combination objective.
I realize there is likely a lot of history here, and I appreciate it is hard to retrospectively fix these things. We have been going through a similar process in GO of removing duplication between MF and BP branches, and it takes time. I appreciate it also takes time to add to the existing excellent but limited visual documentation here (https://obi-ontology.org/docs/core-classes/).
However, for long term maintenance, and to simplify things for users I think it would make sense to commit to either documenting some of the duplication patterns, or to start trimming them down. I'm not totally sure why simply having a process and material entity branch wouldn't suffice for most people who want terms for syringes, injection protocols, etc.